Fig. 3: Sex specificity, timing and species distribution of sexual reproduction markers.

a Bar plot showing the average cross-species log2 fold changes of the top-10 ranked data-driven markers during sexual reproduction. b Boxplots assessing expression specificity by contrasting the expression of data-driven markers during sexual reproduction (n = 8, pink) and other conditions (n = 119, blue) in the S. robusta expression atlas. The central line of the boxplot indicates the median, the box limits show the 25th and 75th percentiles and whiskers extend up to 1.5× the interquartile range. Individual observations are shown as dots. Markers 4, 7 and 8 contain two S. robusta homologs, whose expression is shown side-by-side. c Heatmaps showing gene expression of data-driven markers, flagella markers and the meiotic positive control gene SPO11-2 in bulk RNA-seq datasets of sexual reproduction in four diatom species. Gene expression in normalized counts per million (CPM) of replicates was averaged for each time point. Normalized CPMs are raw CPMs that were scaled to a maximum of one per gene (row-wise). Time points are designated by a letter referring to the corresponding sexual cell stage at that time point. Empty tiles represent sexual stages that were not sampled in a given species. Expression values of the partial gene models making up S. marinoi DNAH9/11/17 were summed. d Taxonomic distribution of sex markers in the genome assemblies of selected diatom species. The size of circles is proportional with the number of gene copies encoded in a species, while their color indicates the taxon each species belongs to.